1. Download the structure of phosphofructose kinase, 3pfk, from the PDB databank. 2. Identify residues that...

 

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1. Download the structure of phosphofructose kinase, 3pfk, from the PDB databank. 2. Identify residues that are within 5A from two phosphate groups in the structure. Extract the picture of the 3D arrangement of these residues. 3. Based on the literature, identify the substrate binding site of pfk. Is the site hydrophobic or hydrophilic? 4. Identify the structural features of the ligand binding site and extract a picture of the active site. Label all residues in the picture. 5. Show the hydrogen bonds within the active site. Are the hydrogen bonds identified by the SWISS PDB Viewer real? Explain. 6. Construct the pfk tetramer based on the symmetry matrix in the pdb file. 7. Merge the pdb files for the tetramer into a new pdb file. 8. Construct molecular surface of the resultant tetramer and extract a picture of the surface. 9. Construct electrostatic map with red, white and blue corresponding to -2, 0, and 2 kT/e, respectively, and paint the molecular surface with the electrostatic potential. Extract a picture of the molecular surface painted by electrostatic potential. 10. What is the electrostatic nature of the substrate binding site? Is it consistent with the predictions from part#3. 1. Download the structure of phosphofructose kinase, 3pfk, from the PDB databank. 2. Identify residues that are within 5A from two phosphate groups in the structure. Extract the picture of the 3D arrangement of these residues. 3. Based on the literature, identify the substrate binding site of pfk. Is the site hydrophobic or hydrophilic? 4. Identify the structural features of the ligand binding site and extract a picture of the active site. Label all residues in the picture. 5. Show the hydrogen bonds within the active site. Are the hydrogen bonds identified by the SWISS PDB Viewer real? Explain. 6. Construct the pfk tetramer based on the symmetry matrix in the pdb file. 7. Merge the pdb files for the tetramer into a new pdb file. 8. Construct molecular surface of the resultant tetramer and extract a picture of the surface. 9. Construct electrostatic map with red, white and blue corresponding to -2, 0, and 2 kT/e, respectively, and paint the molecular surface with the electrostatic potential. Extract a picture of the molecular surface painted by electrostatic potential. 10. What is the electrostatic nature of the substrate binding site? Is it consistent with the predictions from part#3.

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1 Download the structure of phosphofructose kinase 3pfk from the PDB databank Answer The structure of phosphofructose kinase 3pfk can be downloaded from the Protein Data Bank PDB using the PDB accessi... View the full answer